mkg {ccems}R Documentation

Make Generic Model

Description

This function maps network topology information into a generic full spur graph model. If TCC is TRUE (default) it also automatically generates and compiles total concentration constraint C code and stores it in the models subdirectory.

Usage

 mkg(strct,monomerMass=90,TCC=TRUE,activity=FALSE) 

Arguments

strct The thread topology of the equilibrium network (see ccems). The slots of this list structure are: heads which is a character vector of the head nodes of threads of the first site in sites; and sites which is a list of sites where each site is a list of character vectors of non-head thread nodes. Naming conventions are given below under Z.
monomerMass The hub protein's monomer mass in kDa. The default is 90 for the big (R1) subunit of ribonucleotide reductase (RNR).
TCC This is TRUE if total concentration constraints (TCCs) are to be used. If so, model C code is automatically generated and compiled. If TCC is FALSE a rational polynomial model is automatically generated as an R function component of the output. Use of rational polynomial models assumes that the approximations [Xfree] = [XT] are reasonable for all non-hub species X (i.e. ligands).
activity If TRUE data fitted is enzyme activity data. Currently this should be !TCC.

Details

This function is typically the first ccems function called in a script. It creates a list of objects generic to the entire model space, i.e. a model space kernel.

Value

A list comprised of the inputs and the following:

id The biochemical equilibrium system ID. This is the set of single character reactant representations collapsed into one string.
hubChar The first character of the first name in strct. As of ver 1.02 this is no longer a passed option.
Z The names of the hub protein complexes expressed as single character reactant symbols followed by the number of copies of it in the complex. For example, R2t1 is a dimer of R with one bound ligand t, R2t2 is saturated dimer, and R2t0 is ligand free dimer. The choice of the symbol Z for hub complexes derives from its common use as a complex number.
nZ The length of Z. An n in front of a name often implies a length.
atomS A character vector of atom/reactant names where the term atom refers to reactant molecules being indivisible in the system of interest. A capital S at the end of a name implies a string.
nAtomS The length of atomS.
specieS A character vector equal to c(atomS,Z), i.e. the names of all of the chemical species.
nSpecieS The length of specieS.
reactantS A list with component names equal to complex names and values equal to vectors of the atomS that comprise them.
W A dataframe of copy numbers/weights of atoms (column names) in each species (row names).
KdS Subscript names of the dissociation constants, one for each element of Z. Binary K sit in positions of their products and use "_" to separate their reactants; spur edges (e.g. head nodes) take their names from Z.
hdS The names of the head nodes.
hds The positions of the head nodes within the Z vector of complex nodes.
sstime The amount of ODE integration time used to reach steady state when solving TCCs (preset to 1e6). Since integration uses variable step sizes which rapidly become large near steady state, overkill is OK.
rtol An lsoda integration relative error tolerance parameter: rtol=1e-5.
atol An lsoda integration absolute error tolerance parameter: atol=1e-7.
parmsTCC The parameters of the total concentration constraints passed to the .dll (or .so) when using lsoda. These include the total concentrations (i.e. system inputs).
initialStateTCC The initial conditions (default zero) used to solve the TCC ODEs.
dfThread A dataframe of the thread within site and oligo structure.
threads A nested list of the thread structure with threads at the top of the list and their contents and memberships below.
threadsWithinSites A list of threads within sites, i.e. the list indices are sites.
nodesWithinSites A list of non-head nodes within sites.
usedLets A vector of the single characters used to label Kd equivalent threads. Currently, if there is more than one thread, entire threads are either completely equal or all free to be different. If the curtain contains a single thread, then that thread can have patches of contiguous blocks that are equal. Thus, a curtain with n threads has n used letters, but a curtain with one thread has as many used letters as there are nodes in that one thread.
fback A function that maps a vector of free concentrations into a vector of complex concentrations given the current set of complete dissociation constant estimates of the optimization algorithm.
code If TCC = TRUE this is the C code of the TCC ODE right hand side. This code is automatically compiled for use by lsoda.

The TCC flag, which passes unchanged from input to output, is used by simulateData to determine how the expected response surface is to be generated.

Note

Kd and Kj are generic grid and spur edge names, respectively. The name KdS above is thus a grid-like name. That it is used to describe hybrid models that include head node spur edges is consistent with their allowance in a generalized definition of grid graphs.

In the description of KdS above "reactants" is used generically to mean a complex or a ligand, but by far, it refers most often to purified substances of known controlled amounts (i.e. the experimentally manipulated variables or the reactants that are initially present). This common usage is synonymous with the use of "atoms" above, which emphasizes their indivisible building block nature in the non-covalent binding equilibriums of interest.

This work was supported by the National Cancer Institute (K25CA104791).

Author(s)

Tom Radivoyevitch

References

Radivoyevitch, T. (2008) Equilibrium model selection: dTTP induced R1 dimerization. BMC Systems Biology 2, 15.

See Also

ccems,ems

Examples

library(ccems)
topology <- list(  
        heads=c("R1t0","R2t0"),  
        sites=list(       
                s=list(                     # s-site    thread #
                        m=c("R1t1"),        # monomer      1
                        d=c("R2t1","R2t2")  # dimer        2
                )
        )
) 
mkg(topology) 

[Package ccems version 1.02 Index]